Frequently asked questions

How can I annotate an SBML model?

The names in SBML can be chosen arbitrarily; to identify the biological meaning of the model components, semanticSBML requires annotations: species, parameter, compartment, reaction and event tags should be specified by an annotation in a MIRIAM-compliant RDF format according to the proposal by N. LeNovere and A. Finney. If annotations are missing, semanticSBML can be used to add them.

Which kind of annotations can be handled by semanticSBML?

SemanticSBML allows you to assign annotations from various databases listed in the resource file. For automatic matching of elements, it has to rely on cross-references between the databases. Currently, the following databases are supported: Gene Ontology, KEGG Enzyme, KEGG Compound, KEGG Drug, KEGG Reaction, ChEBI and NCBI Taxonomy.

What happens to non-annotated elements during merging?

By default, non-annotated elements are treated as if they had no semantic relation to the other elements, i.e., as individual elements. In the interactive merging process, the user can match them to other elements.

Why cannot I load the database of PubChem?

Probably you do not have checked whether your computer has a RAM of 64 GB. Because if it does not you cannot. We are still working on this condition.